Organism : Bacillus cereus ATCC14579 | Module List :
BC3404

Transcriptional regulator, MarR family (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3404
(Mouseover regulator name to see its description)

BC3404 is regulated by 23 influences and regulates 6 modules.
Regulators for BC3404 (23)
Regulator Module Operator
BC0648 414 tf
BC1059 414 tf
BC1490 414 tf
BC1715 414 tf
BC2988 414 tf
BC3194 414 tf
BC3438 414 tf
BC3690 414 tf
BC3704 414 tf
BC4001 414 tf
BC4211 414 tf
BC4570 414 tf
BC5363 414 tf
BC0224 208 tf
BC0583 208 tf
BC0657 208 tf
BC1531 208 tf
BC2470 208 tf
BC3072 208 tf
BC3404 208 tf
BC3922 208 tf
BC4501 208 tf
BC5265 208 tf

Warning: BC3404 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
4332 4.90e+03 gaaG.gaAaaaagaa..a.tGGA
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4333 7.90e+03 CcTcCCaCGC
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4738 6.20e-02 aaAGGagg
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4739 1.40e+04 GCcGacAatCcCCc
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BC3404

BC3404 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for BC3404

BC3404 has total of 54 gene neighbors in modules 208, 414
Gene neighbors (54)
Gene Common Name Description Module membership
BC0509 BC0509 Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) 394, 414
BC0550 BC0550 hypothetical protein (NCBI ptt file) 200, 208
BC0555 BC0555 Glycine betaine transporter (NCBI ptt file) 15, 414
BC1051 BC1051 Protein ecsB (NCBI ptt file) 117, 208
BC1100 BC1100 hypothetical protein (NCBI ptt file) 208, 427
BC1151 BC1151 IG hypothetical 17028 (NCBI ptt file) 414, 443
BC1311 BC1311 Small acid-soluble spore protein (NCBI ptt file) 208, 460
BC1443 BC1443 SAM-dependent methyltransferase (NCBI ptt file) 414, 431
BC1520 BC1520 hypothetical Cytosolic Protein (NCBI ptt file) 208, 268
BC1597 BC1597 Ribonuclease HI (NCBI ptt file) 381, 414
BC1614 BC1614 Multidrug-efflux transporter 2 regulator (NCBI ptt file) 261, 414
BC2055 BC2055 Macrolide-efflux protein (NCBI ptt file) 194, 414
BC2089 BC2089 hypothetical protein (NCBI ptt file) 208, 525
BC2093 BC2093 hypothetical protein (NCBI ptt file) 208, 460
BC2100 BC2100 Methyltransferase (NCBI ptt file) 113, 208
BC2230 BC2230 Macrolide-efflux protein (NCBI ptt file) 194, 208
BC2277 BC2277 hypothetical protein (NCBI ptt file) 414, 438
BC2449 BC2449 Lipase/Acylhydrolase with GDSL-like motif (NCBI ptt file) 208, 377
BC2707 BC2707 Acetyltransferase (NCBI ptt file) 208, 413
BC3000 BC3000 Proline/betaine transporter (NCBI ptt file) 414, 438
BC3041 BC3041 hypothetical protein (NCBI ptt file) 208, 254
BC3137 BC3137 Deoxyribodipyrimidine photolyase (NCBI ptt file) 208, 254
BC3149 BC3149 1,4-dihydroxy-2-naphthoate octaprenyltransferase (NCBI ptt file) 201, 208
BC3194 BC3194 Transcriptional regulator, MarR family (NCBI ptt file) 414, 511
BC3311 BC3311 hypothetical protein (NCBI ptt file) 414, 505
BC3314 BC3314 Quinolone resistence NorA protein (NCBI ptt file) 298, 414
BC3343 BC3343 Integral membrane protein (NCBI ptt file) 216, 414
BC3344 BC3344 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 343, 414
BC3404 BC3404 Transcriptional regulator, MarR family (NCBI ptt file) 208, 414
BC3413 BC3413 Esterase (NCBI ptt file) 208, 413
BC3414 BC3414 hydrolase (NCBI ptt file) 113, 208
BC3559 BC3559 Chloramphenicol-sensitive protein rarD (NCBI ptt file) 208, 527
BC3624 BC3624 None 208, 439
BC3649 BC3649 None 414, 505
BC3704 BC3704 LexA repressor (NCBI ptt file) 414, 443
BC3711 BC3711 DNA integration/recombination/invertion protein (NCBI ptt file) 194, 414
BC3794 BC3794 hypothetical protein (NCBI ptt file) 414, 430
BC3795 BC3795 Translocation-enhancing protein tepA (NCBI ptt file) 414, 430
BC3935 BC3935 hypothetical Cytosolic Protein (NCBI ptt file) 402, 414
BC4019 BC4019 hypothetical protein (NCBI ptt file) 414, 511
BC4088 BC4088 IG hypothetical 17224 (NCBI ptt file) 257, 414
BC4102 BC4102 Alpha/beta hydrolase (NCBI ptt file) 6, 208
BC4501 BC4501 Germination protein gerE (NCBI ptt file) 13, 208
BC4531 BC4531 hypothetical protein (NCBI ptt file) 288, 414
BC4726 BC4726 hypothetical protein (NCBI ptt file) 385, 414
BC4808 BC4808 Thiamine transporter (NCBI ptt file) 277, 414
BC4817 BC4817 hypothetical protein (NCBI ptt file) 246, 414
BC4819 BC4819 hypothetical protein (NCBI ptt file) 263, 414
BC4862 BC4862 Lipase (NCBI ptt file) 186, 414
BC4958 BC4958 NAD(P)H dehydrogenase [quinone] (NCBI ptt file) 103, 414
BC5379 BC5379 dGTP triphosphohydrolase (NCBI ptt file) 414, 475
BC5418 BC5418 Transporter, MFS superfamily (NCBI ptt file) 385, 414
BC5441 BC5441 Autolysin sensor kinase (NCBI ptt file) 286, 414
BC5459 BC5459 None 208, 445
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for BC3404
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend